2023-09-13T12:03:03,255 Created temporary directory: /tmp/pip-build-tracker-tpgprdnw
2023-09-13T12:03:03,256 Initialized build tracking at /tmp/pip-build-tracker-tpgprdnw
2023-09-13T12:03:03,257 Created build tracker: /tmp/pip-build-tracker-tpgprdnw
2023-09-13T12:03:03,257 Entered build tracker: /tmp/pip-build-tracker-tpgprdnw
2023-09-13T12:03:03,258 Created temporary directory: /tmp/pip-wheel-c9n7nz82
2023-09-13T12:03:03,261 Created temporary directory: /tmp/pip-ephem-wheel-cache-7rcp95h0
2023-09-13T12:03:03,283 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-13T12:03:03,287 2 location(s) to search for versions of py-cortex-api:
2023-09-13T12:03:03,287 * https://pypi.org/simple/py-cortex-api/
2023-09-13T12:03:03,287 * https://www.piwheels.org/simple/py-cortex-api/
2023-09-13T12:03:03,288 Fetching project page and analyzing links: https://pypi.org/simple/py-cortex-api/
2023-09-13T12:03:03,289 Getting page https://pypi.org/simple/py-cortex-api/
2023-09-13T12:03:03,290 Found index url https://pypi.org/simple/
2023-09-13T12:03:03,430 Fetched page https://pypi.org/simple/py-cortex-api/ as application/vnd.pypi.simple.v1+json
2023-09-13T12:03:03,432   Found link https://files.pythonhosted.org/packages/10/9a/15dd2926e462ede2596498e7fdaff6177f47a0a3e0e7d55809a295c7c2e0/py-cortex-api-1.0.tar.gz (from https://pypi.org/simple/py-cortex-api/), version: 1.0
2023-09-13T12:03:03,432   Found link https://files.pythonhosted.org/packages/4f/9b/5df6d4526ebcc12ee6d6a932150243ea6d74e7749b813b898504c51e8fd4/py-cortex-api-2.0.0.tar.gz (from https://pypi.org/simple/py-cortex-api/), version: 2.0.0
2023-09-13T12:03:03,433   Found link https://files.pythonhosted.org/packages/0f/73/39f8d4af8a1819908811755effc9ef16e8a650360e4d9a97aa9f57a24010/py-cortex-api-2.1.0.tar.gz (from https://pypi.org/simple/py-cortex-api/), version: 2.1.0
2023-09-13T12:03:03,434   Found link https://files.pythonhosted.org/packages/8a/0b/c81cf0f0feeda39cc42e7551864635ac911a3312406d3d68e836b1058a5e/py-cortex-api-2.2.0.tar.gz (from https://pypi.org/simple/py-cortex-api/), version: 2.2.0
2023-09-13T12:03:03,435   Found link https://files.pythonhosted.org/packages/85/e6/39478462ebcc183ec04acf85dfda6ef3a6cc3b8dd783b50432014170844f/py-cortex-api-2.2.1.tar.gz (from https://pypi.org/simple/py-cortex-api/), version: 2.2.1
2023-09-13T12:03:03,435 Fetching project page and analyzing links: https://www.piwheels.org/simple/py-cortex-api/
2023-09-13T12:03:03,436 Getting page https://www.piwheels.org/simple/py-cortex-api/
2023-09-13T12:03:03,437 Found index url https://www.piwheels.org/simple/
2023-09-13T12:03:03,766 Fetched page https://www.piwheels.org/simple/py-cortex-api/ as text/html
2023-09-13T12:03:03,767 Skipping link: not a file: https://www.piwheels.org/simple/py-cortex-api/
2023-09-13T12:03:03,767 Skipping link: not a file: https://pypi.org/simple/py-cortex-api/
2023-09-13T12:03:03,786 Given no hashes to check 1 links for project 'py-cortex-api': discarding no candidates
2023-09-13T12:03:03,805 Collecting py-cortex-api==2.2.0
2023-09-13T12:03:03,807   Created temporary directory: /tmp/pip-unpack-rql2urlv
2023-09-13T12:03:04,236   Downloading py-cortex-api-2.2.0.tar.gz (16 kB)
2023-09-13T12:03:04,308   Added py-cortex-api==2.2.0 from https://files.pythonhosted.org/packages/8a/0b/c81cf0f0feeda39cc42e7551864635ac911a3312406d3d68e836b1058a5e/py-cortex-api-2.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-tpgprdnw'
2023-09-13T12:03:04,311   Running setup.py (path:/tmp/pip-wheel-c9n7nz82/py-cortex-api_a66fd3b81d904f2b9bd42dcff27ded42/setup.py) egg_info for package py-cortex-api
2023-09-13T12:03:04,312   Created temporary directory: /tmp/pip-pip-egg-info-5mdd9p9p
2023-09-13T12:03:04,314   Preparing metadata (setup.py): started
2023-09-13T12:03:04,315   Running command python setup.py egg_info
2023-09-13T12:03:05,602   running egg_info
2023-09-13T12:03:05,603   creating /tmp/pip-pip-egg-info-5mdd9p9p/py_cortex_api.egg-info
2023-09-13T12:03:05,627   writing /tmp/pip-pip-egg-info-5mdd9p9p/py_cortex_api.egg-info/PKG-INFO
2023-09-13T12:03:05,631   writing dependency_links to /tmp/pip-pip-egg-info-5mdd9p9p/py_cortex_api.egg-info/dependency_links.txt
2023-09-13T12:03:05,633   writing requirements to /tmp/pip-pip-egg-info-5mdd9p9p/py_cortex_api.egg-info/requires.txt
2023-09-13T12:03:05,634   writing top-level names to /tmp/pip-pip-egg-info-5mdd9p9p/py_cortex_api.egg-info/top_level.txt
2023-09-13T12:03:05,635   writing manifest file '/tmp/pip-pip-egg-info-5mdd9p9p/py_cortex_api.egg-info/SOURCES.txt'
2023-09-13T12:03:05,685   reading manifest file '/tmp/pip-pip-egg-info-5mdd9p9p/py_cortex_api.egg-info/SOURCES.txt'
2023-09-13T12:03:05,686   reading manifest template 'MANIFEST.in'
2023-09-13T12:03:05,690   warning: no files found matching 'cortex/ext/cortex/bin/cortex_var_31_c1'
2023-09-13T12:03:05,690   warning: no files found matching 'cortex/ext/cortex/bin/cortex_var_31_c2'
2023-09-13T12:03:05,691   warning: no previously-included files matching '*~' found anywhere in distribution
2023-09-13T12:03:05,691   warning: no previously-included files matching '*.swp' found anywhere in distribution
2023-09-13T12:03:05,693   writing manifest file '/tmp/pip-pip-egg-info-5mdd9p9p/py_cortex_api.egg-info/SOURCES.txt'
2023-09-13T12:03:05,815   Preparing metadata (setup.py): finished with status 'done'
2023-09-13T12:03:05,820   Source in /tmp/pip-wheel-c9n7nz82/py-cortex-api_a66fd3b81d904f2b9bd42dcff27ded42 has version 2.2.0, which satisfies requirement py-cortex-api==2.2.0 from https://files.pythonhosted.org/packages/8a/0b/c81cf0f0feeda39cc42e7551864635ac911a3312406d3d68e836b1058a5e/py-cortex-api-2.2.0.tar.gz
2023-09-13T12:03:05,821   Removed py-cortex-api==2.2.0 from https://files.pythonhosted.org/packages/8a/0b/c81cf0f0feeda39cc42e7551864635ac911a3312406d3d68e836b1058a5e/py-cortex-api-2.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-tpgprdnw'
2023-09-13T12:03:05,826 Created temporary directory: /tmp/pip-unpack-m5jidcw4
2023-09-13T12:03:05,827 Created temporary directory: /tmp/pip-unpack-qgkmdvt_
2023-09-13T12:03:05,831 Building wheels for collected packages: py-cortex-api
2023-09-13T12:03:05,837   Created temporary directory: /tmp/pip-wheel-wt5p4vrm
2023-09-13T12:03:05,838   Building wheel for py-cortex-api (setup.py): started
2023-09-13T12:03:05,839   Destination directory: /tmp/pip-wheel-wt5p4vrm
2023-09-13T12:03:05,840   Running command python setup.py bdist_wheel
2023-09-13T12:03:07,013   running bdist_wheel
2023-09-13T12:03:07,114   running build
2023-09-13T12:03:07,115   running build_py
2023-09-13T12:03:07,115   START: Building backend dependencies
2023-09-13T12:07:06,462   Cloning into 'minimap2'...
2023-09-13T12:07:06,463   fatal: transport 'https' not allowed
2023-09-13T12:07:06,464   ./cortex/ext/install_dependencies.sh: line 15: cd: minimap2_dir: No such file or directory
2023-09-13T12:07:06,465   mv: cannot stat 'minimap2_dir/minimap2': No such file or directory
2023-09-13T12:07:06,466   --2023-09-13 12:03:07--  https://github.com/vcftools/vcftools/releases/download/v0.1.15/vcftools-0.1.15.tar.gz
2023-09-13T12:07:06,467   Resolving github.com (github.com)... 64:ff9b::8c52:7903, 140.82.121.3
2023-09-13T12:07:06,468   Connecting to github.com (github.com)|64:ff9b::8c52:7903|:443... connected.
2023-09-13T12:07:06,469   HTTP request sent, awaiting response... 302 Found
2023-09-13T12:07:06,469   Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/38052058/2e0f4764-22d4-11e7-8512-08df6111866d?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20230913%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20230913T120307Z&X-Amz-Expires=300&X-Amz-Signature=a4fd0c64044875cae6d80b0710f248869739316d35ed2fd79638a5d523999628&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=38052058&response-content-disposition=attachment%3B%20filename%3Dvcftools-0.1.15.tar.gz&response-content-type=application%2Foctet-stream [following]
2023-09-13T12:07:06,470   --2023-09-13 12:03:07--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/38052058/2e0f4764-22d4-11e7-8512-08df6111866d?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20230913%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20230913T120307Z&X-Amz-Expires=300&X-Amz-Signature=a4fd0c64044875cae6d80b0710f248869739316d35ed2fd79638a5d523999628&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=38052058&response-content-disposition=attachment%3B%20filename%3Dvcftools-0.1.15.tar.gz&response-content-type=application%2Foctet-stream
2023-09-13T12:07:06,471   Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 64:ff9b::b9c7:6f85, 64:ff9b::b9c7:6c85, 64:ff9b::b9c7:6d85, ...
2023-09-13T12:07:06,472   Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|64:ff9b::b9c7:6f85|:443... connected.
2023-09-13T12:07:06,473   HTTP request sent, awaiting response... 200 OK
2023-09-13T12:07:06,473   Length: 481398 (470K) [application/octet-stream]
2023-09-13T12:07:06,474   Saving to: ‘vcftools-0.1.15.tar.gz’

2023-09-13T12:07:06,475        0K .......... .......... .......... .......... .......... 10% 5.10M 0s
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2023-09-13T12:07:06,483   2023-09-13 12:03:08 (8.40 MB/s) - ‘vcftools-0.1.15.tar.gz’ saved [481398/481398]

2023-09-13T12:07:06,484   In file included from /usr/include/c++/12/vector:70,
2023-09-13T12:07:06,485                    from entry.h:12,
2023-09-13T12:07:06,486                    from bcf_entry.h:10,
2023-09-13T12:07:06,487                    from bcf_entry_setters.cpp:9:
2023-09-13T12:07:06,487   /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
2023-09-13T12:07:06,488   /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
2023-09-13T12:07:06,489     523 |     vector<_Tp, _Alloc>::
2023-09-13T12:07:06,489         |     ^~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,490   In file included from /usr/include/c++/12/vector:64:
2023-09-13T12:07:06,491   In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
2023-09-13T12:07:06,492       inlined from ‘void bcf_entry::set_indv_GQUALITY(unsigned int, const float&)’ at bcf_entry_setters.cpp:333:18:
2023-09-13T12:07:06,493   /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2023-09-13T12:07:06,494    1032 |           _M_fill_insert(end(), __new_size - size(), __x);
2023-09-13T12:07:06,495         |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,495   In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
2023-09-13T12:07:06,496       inlined from ‘void bcf_entry::set_indv_GQUALITY(unsigned int, const std::vector<char>&)’ at bcf_entry_setters.cpp:316:18:
2023-09-13T12:07:06,497   /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2023-09-13T12:07:06,498    1032 |           _M_fill_insert(end(), __new_size - size(), __x);
2023-09-13T12:07:06,499         |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,499   In file included from /usr/include/c++/12/bits/stl_algobase.h:64,
2023-09-13T12:07:06,500                    from /usr/include/c++/12/algorithm:60,
2023-09-13T12:07:06,501                    from variant_file.h:15,
2023-09-13T12:07:06,502                    from variant_file_output.cpp:8:
2023-09-13T12:07:06,502   /usr/include/c++/12/bits/stl_pair.h: In instantiation of ‘constexpr std::pair<typename std::__strip_reference_wrapper<typename std::decay<_Tp>::type>::__type, typename std::__strip_reference_wrapper<typename std::decay<_Tp2>::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper<typename decay<_Tp2>::type>::__type = double; typename decay<_Tp2>::type = double; typename __strip_reference_wrapper<typename decay<_Tp>::type>::__type = double; typename decay<_Tp>::type = double]’:
2023-09-13T12:07:06,503   variant_file_output.cpp:4424:39:   required from here
2023-09-13T12:07:06,504   /usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
2023-09-13T12:07:06,505     741 |     make_pair(_T1&& __x, _T2&& __y)
2023-09-13T12:07:06,505         |     ^~~~~~~~~
2023-09-13T12:07:06,506   In file included from /usr/include/c++/12/vector:70,
2023-09-13T12:07:06,507                    from /usr/include/c++/12/functional:62,
2023-09-13T12:07:06,507                    from variant_file.h:24:
2023-09-13T12:07:06,508   /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = std::pair<int, double>; _Alloc = std::allocator<std::pair<int, double> >]’:
2023-09-13T12:07:06,509   /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<std::pair<int, double> >::iterator’ changed in GCC 7.1
2023-09-13T12:07:06,510     523 |     vector<_Tp, _Alloc>::
2023-09-13T12:07:06,511         |     ^~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,512   /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<double, double>}; _Tp = std::pair<double, double>; _Alloc = std::allocator<std::pair<double, double> >]’:
2023-09-13T12:07:06,512   /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<std::pair<double, double> >::iterator’ changed in GCC 7.1
2023-09-13T12:07:06,513     439 |       vector<_Tp, _Alloc>::
2023-09-13T12:07:06,514         |       ^~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,515   /usr/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<double, double>}; _Tp = std::pair<double, double>; _Alloc = std::allocator<std::pair<double, double> >]’:
2023-09-13T12:07:06,516   /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, double>*, std::vector<std::pair<double, double> > >’ changed in GCC 7.1
2023-09-13T12:07:06,516     123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
2023-09-13T12:07:06,517         |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,518   In file included from /usr/include/c++/12/set:60,
2023-09-13T12:07:06,518                    from variant_file.h:26:
2023-09-13T12:07:06,519   /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const double&>, std::tuple<>}; _Key = double; _Val = std::pair<const double, std::pair<unsigned int, unsigned int> >; _KeyOfValue = std::_Select1st<std::pair<const double, std::pair<unsigned int, unsigned int> > >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, std::pair<unsigned int, unsigned int> > >]’:
2023-09-13T12:07:06,520   /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree<double, std::pair<const double, std::pair<unsigned int, unsigned int> >, std::_Select1st<std::pair<const double, std::pair<unsigned int, unsigned int> > >, std::less<double>, std::allocator<std::pair<const double, std::pair<unsigned int, unsigned int> > > >::const_iterator’ changed in GCC 7.1
2023-09-13T12:07:06,521    2457 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
2023-09-13T12:07:06,522         |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,522   In file included from /usr/include/c++/12/map:61,
2023-09-13T12:07:06,523                    from variant_file.h:28:
2023-09-13T12:07:06,524   In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::pair<unsigned int, unsigned int>; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, std::pair<unsigned int, unsigned int> > >]’,
2023-09-13T12:07:06,524       inlined from ‘void variant_file::output_TsTv_by_quality(const parameters&)’ at variant_file_output.cpp:3277:21:
2023-09-13T12:07:06,525   /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<double, std::pair<const double, std::pair<unsigned int, unsigned int> >, std::_Select1st<std::pair<const double, std::pair<unsigned int, unsigned int> > >, std::less<double>, std::allocator<std::pair<const double, std::pair<unsigned int, unsigned int> > > >::const_iterator’ changed in GCC 7.1
2023-09-13T12:07:06,526     511 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
2023-09-13T12:07:06,526         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,527     512 |                                             std::tuple<const key_type&>(__k),
2023-09-13T12:07:06,527         |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,528     513 |                                             std::tuple<>());
2023-09-13T12:07:06,529         |                                             ~~~~~~~~~~~~~~~
2023-09-13T12:07:06,529   In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::pair<unsigned int, unsigned int>; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, std::pair<unsigned int, unsigned int> > >]’,
2023-09-13T12:07:06,530       inlined from ‘void variant_file::output_TsTv_by_quality(const parameters&)’ at variant_file_output.cpp:3279:21:
2023-09-13T12:07:06,531   /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<double, std::pair<const double, std::pair<unsigned int, unsigned int> >, std::_Select1st<std::pair<const double, std::pair<unsigned int, unsigned int> > >, std::less<double>, std::allocator<std::pair<const double, std::pair<unsigned int, unsigned int> > > >::const_iterator’ changed in GCC 7.1
2023-09-13T12:07:06,531     511 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
2023-09-13T12:07:06,532         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,533     512 |                                             std::tuple<const key_type&>(__k),
2023-09-13T12:07:06,533         |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,534     513 |                                             std::tuple<>());
2023-09-13T12:07:06,535         |                                             ~~~~~~~~~~~~~~~
2023-09-13T12:07:06,536   In file included from /usr/include/c++/12/vector:64:
2023-09-13T12:07:06,537   In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = std::pair<int, double>; _Alloc = std::allocator<std::pair<int, double> >]’,
2023-09-13T12:07:06,537       inlined from ‘void variant_file::output_Tajima_D(const parameters&)’ at variant_file_output.cpp:4015:22:
2023-09-13T12:07:06,538   /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >’ changed in GCC 7.1
2023-09-13T12:07:06,539    1032 |           _M_fill_insert(end(), __new_size - size(), __x);
2023-09-13T12:07:06,539         |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,540   In file included from /usr/include/c++/12/vector:70,
2023-09-13T12:07:06,541                    from entry.h:12,
2023-09-13T12:07:06,541                    from vcf_entry.h:12,
2023-09-13T12:07:06,542                    from vcf_entry_setters.cpp:9:
2023-09-13T12:07:06,543   /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
2023-09-13T12:07:06,544   /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
2023-09-13T12:07:06,544     523 |     vector<_Tp, _Alloc>::
2023-09-13T12:07:06,545         |     ^~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,546   In file included from /usr/include/c++/12/vector:64:
2023-09-13T12:07:06,546   In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
2023-09-13T12:07:06,547       inlined from ‘void vcf_entry::set_indv_GQUALITY(unsigned int, double)’ at vcf_entry_setters.cpp:181:18:
2023-09-13T12:07:06,548   /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2023-09-13T12:07:06,549    1032 |           _M_fill_insert(end(), __new_size - size(), __x);
2023-09-13T12:07:06,550         |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-13T12:07:06,550   Cloning into 'cortex'...
2023-09-13T12:07:06,551   fatal: transport 'https' not allowed

2023-09-13T12:07:06,553   ERROR: backend compilation failed 128
2023-09-13T12:07:06,601   ERROR: [present-rich] python setup.py bdist_wheel exited with 255
2023-09-13T12:07:06,614   [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c '
2023-09-13T12:07:06,614   exec(compile('"'"''"'"''"'"'
2023-09-13T12:07:06,614   # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
2023-09-13T12:07:06,614   #
2023-09-13T12:07:06,614   # - It imports setuptools before invoking setup.py, to enable projects that directly
2023-09-13T12:07:06,614   #   import from `distutils.core` to work with newer packaging standards.
2023-09-13T12:07:06,614   # - It provides a clear error message when setuptools is not installed.
2023-09-13T12:07:06,614   # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
2023-09-13T12:07:06,614   #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
2023-09-13T12:07:06,614   #     manifest_maker: standard file '"'"'-c'"'"' not found".
2023-09-13T12:07:06,614   # - It generates a shim setup.py, for handling setup.cfg-only projects.
2023-09-13T12:07:06,614   import os, sys, tokenize
2023-09-13T12:07:06,614   
2023-09-13T12:07:06,614   try:
2023-09-13T12:07:06,614       import setuptools
2023-09-13T12:07:06,614   except ImportError as error:
2023-09-13T12:07:06,614       print(
2023-09-13T12:07:06,614           "ERROR: Can not execute `setup.py` since setuptools is not available in "
2023-09-13T12:07:06,614           "the build environment.",
2023-09-13T12:07:06,614           file=sys.stderr,
2023-09-13T12:07:06,614       )
2023-09-13T12:07:06,614       sys.exit(1)
2023-09-13T12:07:06,614   
2023-09-13T12:07:06,614   __file__ = %r
2023-09-13T12:07:06,614   sys.argv[0] = __file__
2023-09-13T12:07:06,614   
2023-09-13T12:07:06,614   if os.path.exists(__file__):
2023-09-13T12:07:06,614       filename = __file__
2023-09-13T12:07:06,614       with tokenize.open(__file__) as f:
2023-09-13T12:07:06,614           setup_py_code = f.read()
2023-09-13T12:07:06,614   else:
2023-09-13T12:07:06,614       filename = "<auto-generated setuptools caller>"
2023-09-13T12:07:06,614       setup_py_code = "from setuptools import setup; setup()"
2023-09-13T12:07:06,614   
2023-09-13T12:07:06,614   exec(compile(setup_py_code, filename, "exec"))
2023-09-13T12:07:06,614   '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-c9n7nz82/py-cortex-api_a66fd3b81d904f2b9bd42dcff27ded42/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' bdist_wheel -d /tmp/pip-wheel-wt5p4vrm[/]
2023-09-13T12:07:06,615   [bold magenta]cwd[/]: /tmp/pip-wheel-c9n7nz82/py-cortex-api_a66fd3b81d904f2b9bd42dcff27ded42/
2023-09-13T12:07:06,615   Building wheel for py-cortex-api (setup.py): finished with status 'error'
2023-09-13T12:07:06,617   ERROR: Failed building wheel for py-cortex-api
2023-09-13T12:07:06,618   Running setup.py clean for py-cortex-api
2023-09-13T12:07:06,619   Running command python setup.py clean
2023-09-13T12:07:07,813   running clean
2023-09-13T12:07:07,860   'build/lib' does not exist -- can't clean it
2023-09-13T12:07:07,861   'build/bdist.linux-armv7l' does not exist -- can't clean it
2023-09-13T12:07:07,861   'build/scripts-3.11' does not exist -- can't clean it
2023-09-13T12:07:07,983 Failed to build py-cortex-api
2023-09-13T12:07:07,985 ERROR: Failed to build one or more wheels
2023-09-13T12:07:07,986 Exception information:
2023-09-13T12:07:07,986 Traceback (most recent call last):
2023-09-13T12:07:07,986   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
2023-09-13T12:07:07,986     status = run_func(*args)
2023-09-13T12:07:07,986              ^^^^^^^^^^^^^^^
2023-09-13T12:07:07,986   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper
2023-09-13T12:07:07,986     return func(self, options, args)
2023-09-13T12:07:07,986            ^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-13T12:07:07,986   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run
2023-09-13T12:07:07,986     raise CommandError("Failed to build one or more wheels")
2023-09-13T12:07:07,986 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2023-09-13T12:07:07,990 Removed build tracker: '/tmp/pip-build-tracker-tpgprdnw'